Mammalian Fatty Acid Synthase (PDB: 2VZ9)
from Sus scrofa
Created by: Bakhtiar Chaudry
The mammalian fatty
acid synthase (PDB: 2VZ9) from Sus scrofa
is a multienzyme complex that catalyzes all steps of fatty acid synthesis (1).
Fatty acids serve multiple purposes in cells from comprising the various
membranes of the cell in the form of phospholipids to serving as a type of
energy storage in the form of triacylglycerides (1). Cells would not exist if
not for fatty acids which stresses the importance of the enzyme that catalyzes
their synthesis and contributes to lipid biosynthesis. In various other
organisms including bacteria and plants, fatty acid synthesis is accomplished
through multiple single-function proteins (1). However, in animals, the
mammalian fatty acid synthase completes all steps of fatty acid synthesis through
the integration of various domains into one large complex (1). Recent knock-out
experiments in mice have shown that inhibiting the fatty acid synthase inhibits
anchorage-independent cell growth, disables many signal transduction pathways,
and ultimately results in apoptosis (2). This enzyme has also recently become
the target of new therapeutic anticancer drugs due to its elevated levels in
many human carcinomas (3). Inhibition of this enzyme results in selective
apoptosis of cancer cells although the mechanisms are still unclear (3).
However, it is known that the anti-cancer agents target the different catalytic
domains of the fatty acid synthase (3). The immense biological significance of
the mammalian fatty acid synthase underscores the importance of studying both
the structure and function of this protein as well as how to disrupt its functions
through novel therapies in cancer cells.
The mammalian fatty
acid synthase is a homodimer that consists of two subunits dimerized
through homophilic interactions and NADP+ which serves as a ligand
(1). This protein consists of 5,024 residues for a total molecular weight of
544,486 Da and an isoelectric point of 5.98 (4). The two polypeptide chains
each contain the different catalytic domains involved in fatty acid synthesis
including dehydratase, enoyl reductase, ketoreductase, ketoacyl synthase,
thioesterase, and malonyl-acetyl transferase domains (1). Each domain, as its
name suggests, performs a different function in the synthesis pathway (1). The
dehydratase domain removes hydrogen and oxygen from the substrate in the form
of water, the enoyl reductase domain reduces any enol functional groups on the
substrate through the addition of hydrogen, the ketoreductase domain reduces
carbonyl groups on the substrate to alcohols, the ketoacyl synthase domain
forms an acetoacetyl compound in the susbtrate, the thioesterase domain breaks
down thioester groups on the substrate to carboxylic acids and thiols, and the
malonyl-acetyl transferase domain transfers malonyl and acetyl groups to the
substrate (1). NADP+-binding sites are dispersed throughout the enzyme as NADP+ is needed by the different domains.
The secondary structure of mammalian fatty acid synthase consists of alpha helices, beta
sheets, 3/10 helices, and random coils. These structures allow each of the
catalytic domains to perform their specified function. For example, the
malonyl-acetyl transferase domain is composed of an α/β-hydrolase core fold
which creates the active site for that particular domain (1). Each of the other
domains contains special crevices, pockets, folds, and tunnels that bind the
substrate and perform their function (1). In addition, some specific residues
are of particular importance during the function of the fatty acid synthase. His-878, Asp-1033, and His-1037 form a composite active site for the substrate in
the dehydratase domain (1). Hydrogen bonding between Asp-1033 and His-1037
helps to stabilize this active site (1). Interactions of Met-1973 and Lys-1995 help to stabilize the active site of the ketoreductase domain (1). Residues 1651-1794 (Val-1651 to Ile-1794) constitute a Rossman fold used for binding nucleotides while residues 1530-1650 (His-1530 to Ile-1650) and 1795-1858 (Leu-1795 to Glu-1858) constitute a substrate binding portion which also binds
NADP+ in the enoyl reductase domain (1). After the substrate is
bound, Lys-1771 and Asp-1797 protonate it after they are protonated by NADPH (1).
The specific structure the fatty acid synthase helps it perform its function
through the interaction of various residues among themselves and their
interaction with the substrate.
The primary and
tertiary structure of similar proteins can be conserved across various
organisms. For example, it is known that the mammalian fatty acid synthase has
evolutionarily conserved regions also found in the fatty acid synthases of
other organisms, including fungi (1). However, certain amino acid substitutions
impart specific functions to the mammalian fatty acid synthase or cause it to have
particularly stable regions when compared to other fatty acid synthases (1).
These changes in the primary structure also contribute to overall changes in
the tertiary structure. The Position-Specific-Iterated Basic Local Alignment
Search Tool (PSI-BLAST) was used to find proteins with a similar primary
structure to the mammalian fatty acid synthase while the Dali Server was used
to find proteins with a similar tertiary structure to the fatty acid synthase.
PSI-BLAST subjects are assigned an E-value based on gaps between the primary
structure of the subject and the query such that a lower E-value corresponds to
higher similarity in the amino acid sequence (5). The Dali Server calculates
differences in intramolecular distances and assigns a Z-score to the comparison
proteins such that a higher Z-score indicates similar folds to the query (6).
An E-value of less than 0.05 and a Z-score greater than 2.0 were considered
significant (5,6). Using these two servers, proteins with similar primary and
tertiary structure were obtained for comparison to the mammalian fatty acid
synthase.
The human fatty acid
synthase is another 540 kDa multienzyme complex present in humans which
performs similar functions as the mammalian fatty acid synthase (7). The
ketosynthase and malonyl-acetyl transferase domains of the human fatty acid
synthase (PDB: 3HHD) are considered as a separate subunit here. It obtained an
E-value of 0.0 (< 0.05) from the PSI-BLAST database and a Z-score of 68.0
(> 2.0) from the Dali Server indicating high primary and tertiary structure
similarities between similar domains on the mammalian fatty acid synthase (5,6).
This shows that the structure and function of fatty acid synthases is conserved
between the mammalian and human lineages. This makes sense evolutionarily
because humans evolved from mammals which means the human fatty acid synthase
evolved from the mammalian fatty acid synthase and retained many of the same
domains. These domains perform the same function in the human fatty acid synthase
as they do in the mammalian version which would explain the similar primary and
tertiary structures. Superimposing both fatty acid synthases visually shows their structural similarities. Another similar
protein is 6-deoxyerthronolide B synthase (PDB: 2HG4) which is also a homodimer.
This polyketide synthase from Saccharopolyspora
erythraea consists of a ketosynthase domain and an acyl transferase domain
which are structurally similar to the same domains in the mammalian fatty acid
synthase (8). An E-value of 0.0 (< 0.05) from PSI-BLAST and a Z-score of
52.1 (> 2.0) from the Dali Server quantitatively confirm the structural
similarity between 6-deoxyerthronolide B synthase and the mammalian fatty acid
synthase (5,6). Again, for the same reason as before, these domains perform the
same function which explains the similar primary and tertiary structures.